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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses
PLoS ONE, Volume 9, No. 6, Article e97338, Year 2014
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Description
Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. © 2014 Ferreira et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC4055538/bin/pone.0097338.s001.tif
https://efashare.b-cdn.net/share/pmc/articles/PMC4055538/bin/pone.0097338.s002.tif
https://efashare.b-cdn.net/share/pmc/articles/PMC4055538/bin/pone.0097338.s003.tif
https://efashare.b-cdn.net/share/pmc/articles/PMC4055538/bin/pone.0097338.s004.xls
https://efashare.b-cdn.net/share/pmc/articles/PMC4055538/bin/pone.0097338.s005.doc
Authors & Co-Authors
Ferreira, Ari José Scattone
Egypt, New Cairo
School of Sciences and Engineering
Siam, Rania
Egypt, New Cairo
School of Sciences and Engineering
Setubal, João Carlos
Brazil, Sao Paulo
Universidade de São Paulo
Moustafa, Ahmed M.
Egypt, New Cairo
School of Sciences and Engineering
Sayed, Ahmed Abdel Aziz
Egypt, New Cairo
School of Sciences and Engineering
Chambergo, Felipe S.
Brazil, Sao Paulo
Universidade de São Paulo
Dawe, Adam S.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Ghazy, Mohamed Abd El Hady
Egypt, New Cairo
School of Sciences and Engineering
Sharaf, Hazem
Egypt, New Cairo
School of Sciences and Engineering
Ouf, Amged A.
Egypt, New Cairo
School of Sciences and Engineering
Alam, Intikhab S.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Abdel-Haleem, Alyaa M.
Egypt, New Cairo
School of Sciences and Engineering
Lehväslaiho, Heikki O.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Ramadan, Eman
Egypt, New Cairo
School of Sciences and Engineering
Antunes, André
Portugal, Braga
Universidade do Minho
Stingl, Ulrich
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Archer, John A.C.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Jankovic, Boris R.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Sogin, Mitchell L.
United States, Woods Hole
Marine Biological Laboratory
Bajic, Vladimir B.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
El-Dorry, Hamza A.A.
Egypt, New Cairo
School of Sciences and Engineering
Statistics
Citations: 45
Authors: 21
Affiliations: 5
Identifiers
Doi:
10.1371/journal.pone.0097338
e-ISSN:
19326203
Research Areas
Environmental
Genetics And Genomics